Six hours after Discovery's launch, Ulysses was deployed from the payload bay. Ulysses, a joint project between the European Space Agency and NASA, was the first spacecraft to study the Sun's polar regions. Its voyage to the Sun began with a sixteen month trip to Jupiter where the planet's gravitational energy was used to fling Ulysses southward out of the orbital plane of the planets and on toward a solar south pole passage in 1994. The spacecraft crossed back over the orbital plane and made a solar north pole passage in 1995. By the time Discovery touched down at Edwards Air Force Base, Ulysses had already traversed one million miles (1.6 Gm) on its five-year mission.

With Ulysses on its way, the STS-41 crew began an ambitious schedule of science experiments. Flowering plant samples were grown in the CHROMEX-2 module in a Kennedy Space Center and State University of New York at Stony Brook experiment. An earlier version of the experiment flown on STS-29 revealed chromosome damage in root tip cells but no damage to control plants on Earth. By studying plant samples carried on Discovery, researchers hoped to determine how the genetic material in the root cells respond to microgravity. The information gained was of importance to future space travelers on long-term expeditions, researchers on the planned Space Station Freedom, and may contribute to advances in intensive farming practices on Earth.

Understanding fire behavior in microgravity was part of the continuing research to improve Space Shuttle safety. In a specially designed chamber, called the Solid Surface Combustion Experiment, a strip of paper was burned and filmed to gain an understanding of the development of flame and its movement in the absence of convection currents. This experiment was sponsored by the Lewis Research Center and Mississippi State University.

Atmospheric ozone depletion is an environmental problem of worldwide concern. At the time, NASA's NIMBUS-7 satellite and NOAA'sTIROS satellites provided daily data to permit researchers to detect ozone trends. The Shuttle Solar Backscatter Ultraviolet Instrument, from the Goddard Space Flight Center, carried an ozone detector instrument identical to those on the satellites. By comparing Discovery's measurements with coordinated satellite observations, scientists were able to calibrate their satellite instruments to insure the most accurate readings possible.

In 1990, a commercial expendable launch vehicle stranded an INTELSAT VI communication satellite in low orbit. Before STS-41, NASA was evaluating a possible Shuttle rescue mission in 1992. In preparation for this rescue, solar arrays, similar to those on the satellite, were exposed to the conditions of low orbit to determine if they were in any way altered by the atomic oxygen present. When the returned arrays were closely examined, it was found that the arrays were not significantly damaged. Based on this finding, NASA went ahead and carried out STS-49 in 1992.

Until STS-41, previous research had shown that during the process of adapting to microgravity, animals and humans experienced loss of bone mass, cardiac deconditioning, and after prolonged periods (over 30 days), developed symptoms similar to that of terrestrial disuse osteoporsis. The goal of the STS-41 Physiological Systems Experiment, sponsored by the Ames Research Center and Pennsylvania State University's Center for Cell Research, was to determine if pharmacological treatments would be effective in reducing or eliminating some of these disorders. Proteins, developed by Genentech of San Francisco, California, were administered to eight rats during the flight while another eight rats accompanying them on the flight did not receive the treatment.

20 September 1990 – Rare view of two space shuttles (STS-35 & STS-41) on adjacent KSC Launch Complex 39 pads. Discovery is on LC-39B in the background, Columbia is on LC-39A in the foreground.

The Investigations into Polymer Membrane Processing experiment was conducted to determine the role convection currents play in membrane formation. Membranes are used in commercial applications for purification of medicines, kidney dialysis, and water desalination. This experiment was sponsored in part by the Battelle Advanced Materials Center for the Commercial Development of Space in Columbus, OH.

During open periods in the STS-41 crew schedule, the astronauts video taped a number of demonstrations as part of an effort to create an educational video tape for middle school level students. The tape was later distributed nationwide through NASA's Teacher Resource Center network.

Additional crew activities included experimenting with a voice command system to control onboard television cameras and monitoring ionizing radiation exposure to the crew within the orbiter cabin.

On 10 October 1990, at 6:57:18 am PDT, Discovery landed at Edwards Air Force Base, CA on runway 22. Rollout distance was 8,276 feet (2,523 m) and the rollout time was 49 seconds (including a braking test). Discovery was returned to Kennedy Space Center on 16 October 1990.

NASA began a tradition of playing music to astronauts during the Gemini program, which was first used to wake up a flight crew during Apollo 15. Each track is specially chosen, often by their families, and usually has a special meaning to an individual member of the crew, or is applicable to their daily activities.[2]